Thirteen flights were cancelled and 82 were rescheduled, a senior Airports Authority of India (AAI) official said.
Eight flights scheduled to depart from Kolkata and five flights which were slated for arrival had been cancelled till 3.30 pm, the senior official said.
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The situation will change only if the weather conditions improve, he said.
The continuous rain, which started late last night, not only affected flights but also resulted in waterlogging in and around the airport.
NSCBIA Director Atul Dikshit told PTI that while some domestic flights from the city to other destinations were cancelled due to the weather, some incoming flights were diverted to different airports after they failed to land here amid gusty winds.
National carrier Air India said five of its incoming flights could not land at the airport here because of the strong winds and were diverted to other destinations.
While Delhi-Kolkata and Delhi-Mumbai flights were diverted to Delhi and Ranchi respectively, a flight from Port Blair was diverted to Agartala.
A flight from Silchar to Kolkata had to land at Guwahati and the flight from Agartala to Kolkata had to return, the spokesperson added.
Only a flight from Hyderabad to Kolkata could land here this morning, he said.
Some private airlines also cancelled flights, airport sources said.
There was waterlogging on the approach road in front of the ramp that leads to the terminal's departure area as well as in the operational area, an airline official said, adding that the water was ankle-length deep.
Sources said an uprooted tree had blocked the approach road to the airport's terminal building.
Traffic snarls as a result of waterlogging in various parts of the city worsened the situation, with passengers getting delayed in reaching the airport.
People who landed at Kolkata airport found it equally difficult to reach their respective destinations, a traffic police officer said.
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